CoV-GLUE | Mutations | Mutation
Details of the codons used for the mutation across all lineages (CodonProp is the proportion each codon is used for this AA mutation):
ORF | CodonNum | Mut | ORF1abMut | MutType | RefCodon | MutCodon | AACount | CodonCount | CodonProp | Genome Position |
ORF1ab/nsp3 | 54 | A54V | A872V | nonsyn | gCc | gTc | 1101 | 1099 | 0.998183 | 2879-2881 |
Details of the mutation no within lineages (LineageCodonProp is the proportion the codon is observed at, at this particular site, on each lineage):
ORF | CodonNum | Mut | RefCodon | MutCodon | CodonCount | AACount | Lineage | LineageCodonProp |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1099 | 1101 | All | 0.00021 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 186 | 186 | B.1.1.7 | 0.000167 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 101 | 101 | AY.103 | 0.000627 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 87 | 87 | AY.23 | 0.006068 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 72 | 72 | B.1.429 | 0.001694 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 70 | 70 | B.1.377 | 0.319635 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 67 | 67 | B.1.569 | 0.971014 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 50 | 50 | B.1 | 0.000458 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 50 | 50 | B.1.1.274 | 0.252525 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 37 | 37 | AY.4 | 0.000058 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 32 | 32 | B.1.617.2 | 0.00012 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 31 | 31 | AY.43 | 0.000137 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 18 | 18 | B.1.2 | 0.000158 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 16 | 16 | AY.102 | 0.000424 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 14 | 14 | AQ.1 | 1 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 13 | 13 | P.1.15 | 0.00302 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 12 | 12 | AY.39 | 0.000297 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 12 | 12 | AY.5 | 0.000248 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 12 | 12 | B.1.1 | 0.000218 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 12 | 12 | B.1.1.37 | 0.002314 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 11 | 11 | AY.4.2 | 0.000239 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 10 | 10 | AY.12 | 0.003161 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 8 | 8 | AY.44 | 0.000049 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 8 | 8 | AY.98.1 | 0.000387 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 7 | 7 | AY.47 | 0.000218 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 7 | 7 | AY.9.1 | 0.000586 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 7 | 7 | B.1.1.434 | 0.00244 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 7 | 7 | B.1.177 | 0.000092 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 7 | 7 | B.1.596 | 0.00061 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 7 | 7 | P.1 | 0.00011 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 5 | 5 | B.1.422 | 0.004062 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 2 | 4 | 0.111111 | |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 4 | 4 | AY.25 | 0.000024 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 4 | 4 | AY.3 | 0.00004 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 4 | 4 | B.1.1.519 | 0.000159 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 4 | 4 | B.1.234 | 0.000528 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 3 | 3 | A.2.5.2 | 0.004717 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 3 | 3 | AY.75 | 0.000168 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 3 | 3 | AY.92 | 0.000862 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 3 | 3 | B.1.243 | 0.000209 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 3 | 3 | B.1.258 | 0.0002 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 3 | 3 | B.1.459 | 0.012245 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 3 | 3 | B.1.509 | 0.002597 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 3 | 3 | B.1.639 | 0.065217 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 2 | 2 | AY.100 | 0.000092 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 2 | 2 | AY.116 | 0.000574 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 2 | 2 | AY.118 | 0.000125 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 2 | 2 | AY.119 | 0.000071 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 2 | 2 | AY.20 | 0.000078 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 2 | 2 | AY.33 | 0.000134 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 2 | 2 | AY.39.1 | 0.000079 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 2 | 2 | AY.46.4 | 0.000329 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 2 | 2 | AY.9.2 | 0.000073 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 2 | 2 | B | 0.000256 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 2 | 2 | B.1.1.214 | 0.000111 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 2 | 2 | B.1.1.63 | 0.000772 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 2 | 2 | B.1.160 | 0.000062 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 2 | 2 | B.1.214.2 | 0.001199 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 2 | 2 | B.1.237 | 0.00995 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 2 | 2 | B.1.36.18 | 0.00084 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | AY.117 | 0.000085 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | AY.120 | 0.000037 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | AY.120.2.1 | 0.000498 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | AY.121 | 0.000135 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | AY.16 | 0.00038 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | AY.19 | 0.00114 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | AY.24 | 0.000431 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | AY.36 | 0.000148 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | AY.4.2.1 | 0.000149 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | AY.4.4 | 0.000409 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | AY.53 | 0.000288 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | AY.65 | 0.000533 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | AY.84 | 0.000437 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | AY.9 | 0.000068 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | AY.99.2 | 0.000092 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | B.1.1.176 | 0.000439 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | B.1.1.187 | 0.00885 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | B.1.1.222 | 0.000204 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | B.1.1.25 | 0.000569 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | B.1.1.277 | 0.000759 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | B.1.1.388 | 0.045455 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | B.1.1.517 | 0.006803 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | B.1.1.526 | 0.003546 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | B.1.177.18 | 0.00116 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | B.1.177.4 | 0.000211 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | B.1.177.7 | 0.000165 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | B.1.221 | 0.000071 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | B.1.258.21 | 0.007752 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | B.1.3 | 0.002618 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | B.1.311 | 0.000275 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | B.1.329 | 0.000608 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | B.1.332 | 0.003497 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | B.1.351 | 0.00003 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | B.1.366 | 0.004878 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | B.1.396 | 0.000706 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | B.1.441 | 0.009615 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | B.1.452 | 0.013699 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | B.1.551 | 0.00129 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | B.1.561 | 0.000397 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | B.1.619.1 | 0.000641 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | B.1.621 | 0.000089 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | B.1.623 | 0.000536 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | B.1.84 | 0.020833 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | B.6 | 0.00091 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | B.6.1 | 0.026316 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | D.5 | 0.004975 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | P.1.12 | 0.000484 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | P.2 | 0.000187 |
ORF1ab/nsp3 | 54 | A54V | gCc | gTc | 1 | 1 | R.1 | 0.00009 |
CoV-GLUE is still in development. CoV-GLUE was originally developed as part of COG-UK by Josh Singer using the GLUE framework at the MRC-University of Glasgow Centre for Virus Research (CVR). In 2021 it was redeveloped by Richard Orton to scale to the millions of genome sequences available. We acknowledge support from the MRC (MC_UU_12014/12), WT (220977/Z/20/Z) and UKRI G2P (MR/W005611/1). Please contact Richard Orton with any queries: Richard.Orton@glasgow.ac.uk
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